Tools hive: LSF to Slurm migration #842
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The changes in this PR are part of switching
ensembl-hivefrom version 2.2 to version 2.7, and of migration from LSF to Slurm. They include:beekeeper_manager.plto stop it from passing arbitrary command-line options tobeekeeper.pl(beekeeper.pl in ensembl-hive, which is the script that is eventually called, no longer allows options outside of the ones that it expects).beekeeper.plto fix a problem when it would call itself. You will notice that the old version ofbeekeeper.plhas adocommand, with which it callsbeekeeper.plinensembl-hive. For some reason that remains a mystery, after we switched ensembl-hive to version 2.7, ourbeekeeper.pl(i.e. the one in the public-plugins repo) started calling itself at thedoline instead of callingbeekeeper.plinensembl-hive. I have updated the file to useforkinstead ofdo.ToolsPipeConfig.pmand its subclasses to update the definition of jobs for SLURM